Resource
| Id | TF_ChIP-seq/ENCSR000BIT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BIT [biosample_summary="Homo sapiens H1" and target="TCF12"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF740HPV|/files/ENCFF740HPV/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN215NEP|/analyses/ENCAN215NEP/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF421BPV|/files/ENCFF421BPV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9906036 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TCF12-human and investigated as a transcription factor is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/} ) audit_warning: Processed alignments file {ENCFF269TPC|/files/ENCFF269TPC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10619776 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TCF12-human and investigated as a transcription factor is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/} ) audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF421BPV|/files/ENCFF421BPV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.80. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF421BPV|/files/ENCFF421BPV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 4.86. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BIT | float |
TF_ChIP-seq_ENCSR000BIT |
TF_ChIP-seq ENCSR000BIT [biosample_summary="Homo sapiens H1" and target="TCF12"]
|
 |
[3.56, 351] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 3132594 | 0.10% | 12616 |
| chr1 | 310574 | 0.12% | 1252 |
| chr1_KI270713v1_random | 256 | 0.63% | 1 |
| chr2 | 246876 | 0.10% | 1000 |
| chr3 | 185637 | 0.09% | 746 |
| chr4 | 132869 | 0.07% | 534 |
| chr5 | 172637 | 0.10% | 685 |
| chr6 | 195670 | 0.11% | 782 |
| chr7 | 168051 | 0.11% | 677 |
| chr8 | 128613 | 0.09% | 518 |
| chr9 | 128213 | 0.09% | 518 |
| chr10 | 150887 | 0.11% | 607 |
| chr11 | 163257 | 0.12% | 663 |
| chr12 | 170637 | 0.13% | 689 |
| chr13 | 85322 | 0.07% | 355 |
| chr14 | 93377 | 0.09% | 371 |
| chr15 | 95782 | 0.09% | 393 |
| chr16 | 115156 | 0.13% | 460 |
| chr17 | 163945 | 0.20% | 657 |
| chr18 | 61254 | 0.08% | 244 |
| chr19 | 136367 | 0.23% | 550 |
| chr20 | 92465 | 0.14% | 368 |
| chr21 | 29294 | 0.06% | 122 |
| chr22 | 60264 | 0.12% | 243 |
| chrM | 3840 | 23.18% | 15 |
| chrX | 40327 | 0.03% | 162 |
| chrY | 1024 | <0.01% | 4 |
| 3340 contigs with no values (129019771 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 12616 | 9 | 366 | 248.3 | 256 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF740HPV.bed.gz | 196.59 KB | c24e29c6e2b2b45cbf81d057dd2e7e56 |
| ENCFF740HPV.tabix.bed.gz | 146.6 KB | 2b7a98ad2299a1e4381033f138d876db |
| ENCFF740HPV.tabix.bed.gz.tbi | 100.66 KB | 62da206f9ff84c42715d78a187fd4474 |
| genomic_resource.yaml | 3.82 KB | 6bbd07cb3ce46b4c7cb092e0c0589018 |
| statistics/ |